MolNFT v1 · #157831 · protein
T.ELONGATUS ndh (data-set 2)
6NBX · NAD(P)H-quinone oxidoreductase subunit 1: “T.ELONGATUS ndh (data-set 2)”. Electron microscopy, 1 ligand (SF4), 20 pockets (best druggability 0.88). MolNFT v1 #157831 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NBX
- Type
- protein
- Length
- 3,854 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)H-quinone oxidoreductase subunit 1; NAD(P)H-quinone oxidoreductase subunit 2…
- EC
- 7.1.1.-, 1.6.5.-, 1.6.5.11
- UniProt
- Q8DL32, Q8DMR6, Q8DJ02, Q8DKY0, Q8DL29, Q8DKX9, Q8DL30, Q8DJD9, Q8DL31, Q8DJ01, Q8DKZ4, Q8DKZ3, Q8DLN5, Q8DJU2, Q8DMU4, V5V507, Q8DL61
- Ligands
- SF4
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 18 distinct chains · 49% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD(P)H-quinone oxidoreductase subunit 1 (EC 7.1.1.-) | protein | 335 | 54% helix, 0% strand | Q8DL32 |
| B | NAD(P)H-quinone oxidoreductase subunit 2 (EC 7.1.1.-) | protein | 483 | 66% helix, 2% strand | Q8DMR6 |
| C | NAD(P)H-quinone oxidoreductase subunit 3 (EC 7.1.1.-) | protein | 100 | 65% helix, 3% strand | Q8DJ02 |
| D | NAD(P)H-quinone oxidoreductase chain 4 1 (EC 1.6.5.-) | protein | 504 | 65% helix, 2% strand | Q8DKY0 |
| E | NAD(P)H-quinone oxidoreductase subunit 4L (EC 1.6.5.-) | protein | 101 | 71% helix, 0% strand | Q8DL29 |
| F | NADH dehydrogenase subunit 5 | protein | 655 | 62% helix, 3% strand | Q8DKX9 |
| G | NADH-quinone oxidoreductase subunit J (EC 1.6.5.11) | protein | 191 | 54% helix, 0% strand | Q8DL30 |
| H | NAD(P)H-quinone oxidoreductase subunit H (EC 1.6.5.-) | protein | 392 | 38% helix, 12% strand | Q8DJD9 |
| I | NAD(P)H-quinone oxidoreductase subunit I (EC 1.6.5.-) | protein | 184 | 11% helix, 11% strand | Q8DL31 |
| J | NAD(P)H-quinone oxidoreductase subunit J (EC 1.6.5.-) | protein | 161 | 17% helix, 25% strand | Q8DJ01 |
| K | NAD(P)H-quinone oxidoreductase subunit K (EC 1.6.5.-) | protein | 212 | 24% helix, 12% strand | Q8DKZ4 |
| L | NAD(P)H-quinone oxidoreductase subunit L (EC 1.6.5.-) | protein | 66 | 47% helix, 0% strand | Q8DKZ3 |
| M | NAD(P)H-quinone oxidoreductase subunit M (EC 1.6.5.-) | protein | 111 | 27% helix, 26% strand | Q8DLN5 |
| N | NAD(P)H-quinone oxidoreductase subunit N (EC 1.6.5.-) | protein | 148 | 30% helix, 22% strand | Q8DJU2 |
| O | NAD(P)H-quinone oxidoreductase subunit O (EC 1.6.5.-) | protein | 69 | 4% helix, 33% strand | Q8DMU4 |
| P | Proton-translocating NADH-quinone dehydrogenase subunit P ndhp | protein | 42 | 36% helix, 0% strand | V5V507 |
| Q | Proton-translocating NADH-quinone dehydrogenase subunit Q ndhq | protein | 43 | 58% helix, 0% strand | — |
| S | TLR0636 protein | protein | 57 | 0% helix, 42% strand | Q8DL61 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains I, H, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.88 | 0.89 | 106 | empty |
| 2 | 564 | 0.85 | 0.90 | 65 | empty |
| 3 | 946 | 0.82 | 0.83 | 73 | empty |
| 4 | 997 | 0.78 | 0.79 | 83 | empty |
| 5 | 273 | 0.78 | 0.89 | 27 | empty |
Interfaces
51 interfaces between chains.
- E–G · 3220 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 2674 Ų buried · 16 hydrogen bonds · protein-protein
- B–G · 2556 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 2548 Ų buried · 5 hydrogen bonds · protein-protein
- K–M · 2472 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6NBX · T.elongatus NDH (data-set 2) · the same entry in another collection · chain K against K, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8DL32
- Every structure of UniProt Q8DMR6
- Every structure of UniProt Q8DJ02
- Every structure of UniProt Q8DKY0
- Every structure of UniProt Q8DL29
- Every structure of UniProt Q8DKX9
- Every structure of UniProt Q8DL30
- Every structure of UniProt Q8DJD9
- Every structure of UniProt Q8DL31
- Every structure of UniProt Q8DJ01
- Every structure of UniProt Q8DKZ4
- Every structure of UniProt Q8DKZ3
- Every structure of UniProt Q8DLN5
- Every structure of UniProt Q8DJU2
- Every structure of UniProt Q8DMU4
- Every structure of UniProt V5V507
- Every structure of UniProt Q8DL61
- Elsewhere: RCSB PDB 6NBX · PDBe 6NBX · UniProt Q8DL32 · UniProt Q8DMR6 · UniProt Q8DJ02 · UniProt Q8DKY0 · UniProt Q8DL29 · UniProt Q8DKX9 · UniProt Q8DL30 · UniProt Q8DJD9 · UniProt Q8DL31 · UniProt Q8DJ01 · UniProt Q8DKZ4 · UniProt Q8DKZ3 · UniProt Q8DLN5 · UniProt Q8DJU2 · UniProt Q8DMU4 · UniProt V5V507 · UniProt Q8DL61
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